Former FAW secretary Alun Evans claims Uefa's plans to allow Cardiff to enter Europe if they win the FA Cup could damage the future of Welsh football.
Cup winners usually qualify for Europe but under current rules Cardiff cannot as they are classed as a Welsh club.
However, Uefa are considering handing them a wildcard entry should they beat Portsmouth in the final on 17 May.
Evans says this will damage FAW plans to help Welsh clubs qualify for Europe through Welsh leagues and competitions.
"I think it's a short-term gain for a long-term loss," explained Evans, who outlined plans for the future development of Welsh football in a strategic document he presented to the Welsh FA earlier this year.
"I think now is the time for us to focus on getting the Welsh clubs playing in Europe on a regular basis and that can only be done by acceptance that playing in Welsh competitions is acceptable to Uefa.
606: DEBATE
"I'm not wishing to deny Cardiff City, in fact I would be quite happy to see them play in Europe. I'm just saying these are the disadvantages of taking this quick fix."
In his document entitled 'FAW Strategic Plan 2007-2012', Evans called for Cardiff, Swansea and Wrexham to be permitted to field teams in the Welsh Premier League.
He suggested the three exiled clubs be allowed to continue to play in the English Football League but field second teams in the Welsh Premier.
Assuming these second teams finished high enough in the Welsh Premier to qualify for European competitions, the trio could then provide more powerful Welsh representation in Europe than is currently provided by Welsh Premier clubs.
"I think it's a short-term gain for a long-term loss"
Uefa rules stopped Cardiff, Swansea and Wrexham, plus Colwyn Bay, Merthyr and Newport, from using Welsh competitions to reach Europe when they continued in the English League rather than join the League of Wales when it was established.
Under normal circumstances the FA Cup winners qualify for the Uefa Cup, but Cardiff's problem is that as a Welsh club - although playing in the English league pyramid - they are not affiliated to the English FA.
The Football Association says it will not nominate Cardiff as the Welsh club as a 'guest' team.
However, Uefa president Michel Platini has already expressed his support for Cardiff if they win the Cup, with Uefa spokesman William Gaillard reiterating that support on Monday.
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